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false positive innodb corruption
Posted by: Hugo Ribeiro
Date: January 25, 2016 06:41AM

Hi guys, i keep getting this random restarts with the error below and canĀ“t figure it out wich table is getting this nor nothing.

Im using 5.6.28 version of mysql and currently im using innodb checksum algoritm.
Im posting here also because it seems to be close to this bug but cant figure if it is or not. But it seems to be a generic problem on the solutions.
http://bugs.mysql.com/bug.php?id=73689

My dumps run smoothly every night with mysqldump and with xtrabackup.

Log file:
2016-01-25 11:28:45 7fbb6a1cb700 InnoDB: uncompressed page, stored checksum in field1 0, calculated checksums for field1: crc32 536728786, innodb 1575996416, none 3735928559, stored checksum in field2 0, calculated checksums for field2: crc32 536728786, innodb 1371122432, none 3735928559, page LSN 0 0, low 4 bytes of LSN at page end 0, page number (if stored to page already) 0, space id (if created with >= MySQL-4.1.1 and stored already) 0
InnoDB: Page may be a freshly allocated page
InnoDB: Page directory corruption: supremum not pointed to
2016-01-25 11:28:45 7fbb6a1cb700 InnoDB: Page dump in ascii and hex (16384 bytes):
len 16384; hex 000000000000000000000000000 bunch of 0, 16k

;
InnoDB: End of page dump
2016-01-25 11:28:45 7fbb6a1cb700 InnoDB: uncompressed page, stored checksum in field1 0, calculated checksums for field1: crc32 536728786, innodb 1575996416, none 3735928559, stored checksum in field2 0, calculated checksums for field2: crc32 536728786, innodb 1371122432, none 3735928559, page LSN 0 0, low 4 bytes of LSN at page end 0, page number (if stored to page already) 0, space id (if created with >= MySQL-4.1.1 and stored already) 0
InnoDB: Page may be a freshly allocated page
2016-01-25 11:28:45 7fbb6a1cb700 InnoDB: Assertion failure in thread 140442915878656 in file rem0rec.cc line 577
InnoDB: We intentionally generate a memory trap.
InnoDB: Submit a detailed bug report to http://bugs.mysql.com.
InnoDB: If you get repeated assertion failures or crashes, even
InnoDB: immediately after the mysqld startup, there may be
InnoDB: corruption in the InnoDB tablespace. Please refer to
InnoDB: http://dev.mysql.com/doc/refman/5.6/en/forcing-innodb-recovery.html
InnoDB: about forcing recovery.
11:28:45 UTC - mysqld got signal 6 ;

key_buffer_size=33554432
read_buffer_size=2097152
max_used_connections=23
max_threads=102
thread_count=24
connection_count=23
It is possible that mysqld could use up to
key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 1914231 K bytes of memory
Hope that's ok; if not, decrease some variables in the equation.

Thread pointer: 0xe440f30
Attempting backtrace. You can use the following information to find out
where mysqld died. If you see no messages after this, something went
terribly wrong...
stack_bottom = 7fbb6a1cae40 thread_stack 0x40000
/usr/sbin/mysqld(my_print_stacktrace+0x2c)[0x8d276c]
/usr/sbin/mysqld(handle_fatal_signal+0x461)[0x657f71]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x10340)[0x7fbd77b3e340]
/lib/x86_64-linux-gnu/libc.so.6(gsignal+0x39)[0x7fbd76f7ecc9]
/lib/x86_64-linux-gnu/libc.so.6(abort+0x148)[0x7fbd76f820d8]
/usr/sbin/mysqld[0x97e5bb]
/usr/sbin/mysqld[0x95fc21]
/usr/sbin/mysqld[0xa0c802]
/usr/sbin/mysqld[0x9ae58e]
/usr/sbin/mysqld[0x9bd1a8]
/usr/sbin/mysqld[0x92dbfb]
/usr/sbin/mysqld[0x9375f3]
/usr/sbin/mysqld[0x5681d6]
/usr/sbin/mysqld[0x9b3c18]
/usr/sbin/mysqld[0x902c46]
/usr/sbin/mysqld(_ZN7handler13ha_index_nextEPh+0x5e)[0x59c42e]
/usr/sbin/mysqld(_ZN7handler15read_range_nextEv+0x20)[0x5a0890]
/usr/sbin/mysqld(_ZN7handler21multi_range_read_nextEPPc+0xb2)[0x597f72]
/usr/sbin/mysqld(_ZN18QUICK_RANGE_SELECT8get_nextEv+0x4b)[0x7e25eb]
/usr/sbin/mysqld[0x805c1d]
/usr/sbin/mysqld(_Z12mysql_deleteP3THDP10TABLE_LISTP4ItemP10SQL_I_ListI8st_orderEyy+0xc76)[0x817dd6]
/usr/sbin/mysqld(_Z21mysql_execute_commandP3THD+0x1c7c)[0x6da8ec]
/usr/sbin/mysqld(_ZN18Prepared_statement7executeEP6Stringb+0x395)[0x6f2945]
/usr/sbin/mysqld(_ZN18Prepared_statement12execute_loopEP6StringbPhS2_+0xb8)[0x6f2b78]
/usr/sbin/mysqld(_Z22mysql_sql_stmt_executeP3THD+0xb3)[0x6f31e3]
/usr/sbin/mysqld(_Z21mysql_execute_commandP3THD+0x11ee)[0x6d9e5e]
/usr/sbin/mysqld(_ZN13sp_instr_stmt9exec_coreEP3THDPj+0x53)[0x807143]
/usr/sbin/mysqld(_ZN12sp_lex_instr23reset_lex_and_exec_coreEP3THDPjb+0x21c)[0x8093bc]
/usr/sbin/mysqld(_ZN12sp_lex_instr29validate_lex_and_execute_coreEP3THDPjb+0xb0)[0x809d40]
/usr/sbin/mysqld(_ZN13sp_instr_stmt7executeEP3THDPj+0x298)[0x80a168]
/usr/sbin/mysqld(_ZN7sp_head7executeEP3THDb+0x46b)[0x65e0db]
/usr/sbin/mysqld(_ZN7sp_head17execute_procedureEP3THDP4ListI4ItemE+0x636)[0x661346]
/usr/sbin/mysqld(_Z21mysql_execute_commandP3THD+0x144d)[0x6da0bd]
/usr/sbin/mysqld(_ZN13sp_instr_stmt9exec_coreEP3THDPj+0x53)[0x807143]
/usr/sbin/mysqld(_ZN12sp_lex_instr23reset_lex_and_exec_coreEP3THDPjb+0x21c)[0x8093bc]
/usr/sbin/mysqld(_ZN12sp_lex_instr29validate_lex_and_execute_coreEP3THDPjb+0xb0)[0x809d40]
/usr/sbin/mysqld(_ZN13sp_instr_stmt7executeEP3THDPj+0x298)[0x80a168]
/usr/sbin/mysqld(_ZN7sp_head7executeEP3THDb+0x46b)[0x65e0db]
/usr/sbin/mysqld(_ZN7sp_head17execute_procedureEP3THDP4ListI4ItemE+0x636)[0x661346]
/usr/sbin/mysqld(_Z21mysql_execute_commandP3THD+0x144d)[0x6da0bd]
/usr/sbin/mysqld(_Z11mysql_parseP3THDPcjP12Parser_state+0x598)[0x6dfdb8]
/usr/sbin/mysqld(_Z16dispatch_command19enum_server_commandP3THDPcj+0x106f)[0x6e15bf]
/usr/sbin/mysqld(_Z24do_handle_one_connectionP3THD+0x162)[0x6aded2]
/usr/sbin/mysqld(handle_one_connection+0x40)[0x6adfc0]
/usr/sbin/mysqld(pfs_spawn_thread+0x143)[0xae9b23]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x8182)[0x7fbd77b36182]
/lib/x86_64-linux-gnu/libc.so.6(clone+0x6d)[0x7fbd7704300d]

Trying to get some variables.
Some pointers may be invalid and cause the dump to abort.
Query (7fbaf415fdb8): is an invalid pointer
Connection ID (thread ID): 23
Status: NOT_KILLED

160125 11:28:46 mysqld_safe Number of processes running now: 0
160125 11:28:46 mysqld_safe mysqld restarted
2016-01-25 11:28:46 0 [Warning] 'THREAD_CONCURRENCY' is deprecated and will be removed in a future release.
2016-01-25 11:28:46 0 [Warning] option 'slow_query_log': boolean value '2' wasn't recognized. Set to OFF.
2016-01-25 11:28:46 0 [Warning] Using unique option prefix key_buffer instead of key_buffer_size is deprecated and will be removed in a future release. Please use the full name instead.
2016-01-25 11:28:46 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2016-01-25 11:28:46 0 [Note] /usr/sbin/mysqld (mysqld 5.6.28-76.1-log) starting as process 3459 ...
2016-01-25 11:28:46 3459 [Warning] Using unique option prefix myisam_recover instead of myisam-recover-options is deprecated and will be removed in a future release. Please use the full name instead.
2016-01-25 11:28:46 3459 [Note] InnoDB: Using atomics to ref count buffer pool pages
2016-01-25 11:28:46 3459 [Note] InnoDB: The InnoDB memory heap is disabled
2016-01-25 11:28:46 3459 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2016-01-25 11:28:46 3459 [Note] InnoDB: Memory barrier is not used
2016-01-25 11:28:46 3459 [Note] InnoDB: Compressed tables use zlib 1.2.8
2016-01-25 11:28:46 3459 [Note] InnoDB: Using Linux native AIO
2016-01-25 11:28:46 3459 [Note] InnoDB: Using CPU crc32 instructions
2016-01-25 11:28:46 3459 [Note] InnoDB: Initializing buffer pool, size = 7.0G
2016-01-25 11:28:47 3459 [Note] InnoDB: Completed initialization of buffer pool
2016-01-25 11:28:47 3459 [Note] InnoDB: Highest supported file format is Barracuda.
2016-01-25 11:28:47 3459 [Note] InnoDB: Log scan progressed past the checkpoint lsn 1340720769666
2016-01-25 11:28:47 3459 [Note] InnoDB: Database was not shutdown normally!
2016-01-25 11:28:47 3459 [Note] InnoDB: Starting crash recovery.
2016-01-25 11:28:47 3459 [Note] InnoDB: Reading tablespace information from the .ibd files...
2016-01-25 11:28:47 3459 [Note] InnoDB: Restoring possible half-written data pages
2016-01-25 11:28:47 3459 [Note] InnoDB: from the doublewrite buffer...
InnoDB: Doing recovery: scanned up to log sequence number 1340726012416
InnoDB: Doing recovery: scanned up to log sequence number 1340726362806
InnoDB: 1 transaction(s) which must be rolled back or cleaned up
InnoDB: in total 1 row operations to undo
InnoDB: Trx id counter is 3655983104
2016-01-25 11:28:49 3459 [Note] InnoDB: Starting an apply batch of log records to the database...
InnoDB: Progress in percent: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
InnoDB: Apply batch completed
InnoDB: Last MySQL binlog file position 0 1624, file name mysql-bin.000026
2016-01-25 11:28:50 3459 [Note] InnoDB: 128 rollback segment(s) are active.
InnoDB: Starting in background the rollback of uncommitted transactions
2016-01-25 11:28:50 7f0c94453700 InnoDB: Rolling back trx with id 3655982521, 1 rows to undo
2016-01-25 11:28:50 3459 [Note] InnoDB: Waiting for purge to start
2016-01-25 11:28:50 3459 [Note] InnoDB: Percona XtraDB (http://www.percona.com) 5.6.28-76.1 started; log sequence number 1340726362806
2016-01-25 11:28:50 3459 [Note] Recovering after a crash using /mnt/sqllogs/mysql/mysql-bin
2016-01-25 11:28:50 3459 [Note] Starting crash recovery...
2016-01-25 11:28:50 3459 [Note] Crash recovery finished.
2016-01-25 11:28:50 3459 [Note] RSA private key file not found: /mnt/sqldata/mysql//private_key.pem. Some authentication plugins will not work.
2016-01-25 11:28:50 3459 [Note] RSA public key file not found: /mnt/sqldata/mysql//public_key.pem. Some authentication plugins will not work.
2016-01-25 11:28:50 3459 [Note] Server hostname (bind-address): '*'; port: 3306
2016-01-25 11:28:50 3459 [Note] IPv6 is available.
2016-01-25 11:28:50 3459 [Note] - '::' resolves to '::';
2016-01-25 11:28:50 3459 [Note] Server socket created on IP: '::'.
2016-01-25 11:28:50 3459 [Warning] 'user' entry '@dina' ignored in --skip-name-resolve mode.
2016-01-25 11:28:50 3459 [Warning] 'proxies_priv' entry '@ root@dina' ignored in --skip-name-resolve mode.
2016-01-25 11:28:50 3459 [Note] InnoDB: Rollback of trx with id 3655982521 completed
2016-01-25 11:28:50 7f0c94453700 InnoDB: Rollback of non-prepared transactions completed
2016-01-25 11:28:50 3459 [Note] Event Scheduler: Loaded 1 event
2016-01-25 11:28:50 3459 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.6.28-76.1-log' socket: '/var/run/mysqld/mysqld.sock' port: 3306 Percona Server (GPL), Release 76.1, Revision 5759e76
2016-01-25 11:28:50 3459 [Note] Event Scheduler: scheduler thread started with id 1
2016-01-25 11:28:51 3459 [ERROR] /usr/sbin/mysqld: Table './mybd/myisamFullIndexCatalog' is marked as crashed and should be repaired
2016-01-25 11:28:51 3459 [Warning] Checking table: './mybd/myisamFullIndexCatalog'

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false positive innodb corruption
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January 25, 2016 06:41AM


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